data_2VSI # _model_server_result.job_id IBiwyXHQJ2JaJZ8R4kj6Dg _model_server_result.datetime_utc '2025-09-03 23:28:32' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2vsi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1234}' # _entry.id 2VSI # _exptl.entry_id 2VSI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-ALPHA-D-ARABINOFURANOSYL}PYRIMIDIN-2(1H)-ONE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2VSI _cell.length_a 80.94 _cell.length_b 92.38 _cell.length_c 143.58 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VSI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id OE2 _struct_conn.ptnr1_label_comp_id GLU _struct_conn.ptnr1_label_seq_id 106 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLU _struct_conn.ptnr1_auth_seq_id 105 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id CA _struct_conn.ptnr2_label_comp_id CA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CA _struct_conn.ptnr2_auth_seq_id 1234 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.8 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDF _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-ALPHA-D-ARABINOFURANOSYL}PYRIMIDIN-2(1H)-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O3B PB CDF doub 70 n n PB O1B CDF sing 71 n n PB O2B CDF sing 72 n n PB O3A CDF sing 73 n n O3A PA CDF sing 74 n n PA O1A CDF sing 75 n n PA O2A CDF doub 76 n n PA O5' CDF sing 77 n n O5' C5' CDF sing 78 n n C5' C4' CDF sing 79 n n C4' O4' CDF sing 80 n n C4' C3' CDF sing 81 n n O4' C1' CDF sing 82 n n C3' O3' CDF sing 83 n n C3' C2' CDF sing 84 n n C2' O2' CDF sing 85 n n C2' C1' CDF sing 86 n n C1' N1 CDF sing 87 n n N1 C2 CDF sing 88 n n N1 C6 CDF sing 89 n n C2 O2 CDF doub 90 n n C2 N3 CDF sing 91 n n N3 C4 CDF doub 92 n n C4 N4 CDF sing 93 n n C4 C5 CDF sing 94 n n O1B H1B CDF sing 95 n n O2B H2B CDF sing 96 n n O1A H1A CDF sing 97 n n C5' "H5'1" CDF sing 98 n n C5' "H5'2" CDF sing 99 n n C4' H4' CDF sing 100 n n C3' H3' CDF sing 101 n n C1' H1' CDF sing 102 n n O3' HA CDF sing 103 n n C2' H2' CDF sing 104 n n O2' HB CDF sing 105 n n N4 H41N CDF sing 106 n n N4 H42N CDF sing 107 n n C6 C5 CDF doub 108 n n C5 H5 CDF sing 109 n n C6 H6 CDF sing 110 n n # _atom_sites.entry_id 2VSI _atom_sites.fract_transf_matrix[1][1] 0.012355 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010825 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006965 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 CDF A 1 1234 1234 CDF CDF . D 2 CDF B 1 1233 1233 CDF CDF . E 3 CA B 1 1234 1234 CA CA . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O3B CDF . . . C 2 -15.604 -14.502 4.27 1 99.09 ? O3B CDF 1234 A 1 HETATM 2 P PB CDF . . . C 2 -15.355 -14.868 2.822 1 98.99 ? PB CDF 1234 A 1 HETATM 3 O O1B CDF . . . C 2 -16.59 -15.353 2.089 1 99.17 ? O1B CDF 1234 A 1 HETATM 4 O O2B CDF . . . C 2 -14.146 -15.758 2.614 1 98.88 ? O2B CDF 1234 A 1 HETATM 5 O O3A CDF . . . C 2 -15.026 -13.452 2.094 1 97.54 ? O3A CDF 1234 A 1 HETATM 6 P PA CDF . . . C 2 -13.668 -12.593 2.311 1 95.75 ? PA CDF 1234 A 1 HETATM 7 O O1A CDF . . . C 2 -13.701 -11.391 1.391 1 95.48 ? O1A CDF 1234 A 1 HETATM 8 O O2A CDF . . . C 2 -13.507 -12.355 3.793 1 95.73 ? O2A CDF 1234 A 1 HETATM 9 O O5' CDF . . . C 2 -12.536 -13.623 1.782 1 94.58 ? O5' CDF 1234 A 1 HETATM 10 C C5' CDF . . . C 2 -11.166 -13.252 1.625 1 92.23 ? C5' CDF 1234 A 1 HETATM 11 C C4' CDF . . . C 2 -10.565 -13.74 0.31 1 90.39 ? C4' CDF 1234 A 1 HETATM 12 O O4' CDF . . . C 2 -11.566 -13.944 -0.696 1 89.59 ? O4' CDF 1234 A 1 HETATM 13 C C3' CDF . . . C 2 -9.64 -12.646 -0.203 1 89.79 ? C3' CDF 1234 A 1 HETATM 14 O O3' CDF . . . C 2 -8.295 -13.119 -0.308 1 89.74 ? O3' CDF 1234 A 1 HETATM 15 C C2' CDF . . . C 2 -10.222 -12.216 -1.536 1 89.4 ? C2' CDF 1234 A 1 HETATM 16 O O2' CDF . . . C 2 -10.134 -10.794 -1.635 1 88.8 ? O2' CDF 1234 A 1 HETATM 17 C C1' CDF . . . C 2 -11.662 -12.719 -1.419 1 89.35 ? C1' CDF 1234 A 1 HETATM 18 N N1 CDF . . . C 2 -12.513 -12.729 -2.633 1 89.31 ? N1 CDF 1234 A 1 HETATM 19 C C2 CDF . . . C 2 -12.106 -13.097 -3.946 1 89.14 ? C2 CDF 1234 A 1 HETATM 20 O O2 CDF . . . C 2 -10.955 -13.488 -4.209 1 89.45 ? O2 CDF 1234 A 1 HETATM 21 N N3 CDF . . . C 2 -12.989 -13.031 -4.968 1 89.12 ? N3 CDF 1234 A 1 HETATM 22 C C4 CDF . . . C 2 -14.259 -12.613 -4.767 1 89.23 ? C4 CDF 1234 A 1 HETATM 23 N N4 CDF . . . C 2 -15.117 -12.558 -5.805 1 89.23 ? N4 CDF 1234 A 1 HETATM 24 C C6 CDF . . . C 2 -13.778 -12.314 -2.446 1 89.52 ? C6 CDF 1234 A 1 HETATM 25 C C5 CDF . . . C 2 -14.684 -12.242 -3.499 1 89.33 ? C5 CDF 1234 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #